• analyze
  • Researchers analyze whether the majority of genes in the set fall in the extremes of this list: the top and bottom of the list correspond to the largest differences in expression between the two cell types. (wikipedia.org)
  • This allows the researcher to analyze regulatory data using their own conditions as to the suitability of the supporting evidence. (wikipedia.org)
  • To achieve this goal, scientists at the Icahn Institute for Genomics and Multiscale Biology have outfitted facilities such as the Genomics Core with new technologies to generate many types of biological information and have placed an emphasis on hiring staff with bioinformatics expertise to analyze big data. (wikipedia.org)
  • systems biology
  • Eric's group has worked with the Institute for Systems Biology (ISB) in Seattle to develop software to display their network. (macdevcenter.com)
  • One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. (mdpi.com)
  • While the assumption of Boolean logic is important for systems biology, detailed studies show that in general the logic of gene regulation is not Boolean. (wikipedia.org)
  • Systems Biology research includes dynamic gene regulatory networks and systems neuroscience. (wikipedia.org)
  • Gary Stormo, Member - Scientific Advisory Board - Systems Biology, Gene Network Sciences Inc". Retrieved 16 January 2014. (wikipedia.org)
  • molecular
  • Bioinformatics methods could help us develop a better understanding of the molecular mechanism of CLL. (spandidos-publications.com)
  • Yet another line of research pertains to Molecular Evolution, which includes evolution of the exonic structure of genes and splicing. (wikipedia.org)
  • Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer. (wikipedia.org)
  • She was awarded the ISCB Overton Prize in 2014 for her significant contribution to research, particularly in using computational methods to understand the organization and function of molecular networks in cells. (wikipedia.org)
  • regulate
  • Cis-regulatory module (CRM) is a stretch of DNA, usually 100-1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. (wikipedia.org)
  • One cis-regulatory element can regulate several genes, and conversely, one gene can have several cis-regulatory modules.Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given. (wikipedia.org)
  • diseases
  • Gene Prediction and Modeling of Splicing is related to the research on Regulation of Alternative Splicing, Regulation of Protein Synthesis within the Gene Regulation program, and Genes and Diseases program. (wikipedia.org)
  • However, this method of comparison is not sensitive enough to detect the subtle differences between the expression of individual genes, because diseases typically involve entire groups of genes. (wikipedia.org)
  • Its aim is to generate and integrate many layers of biological, clinical, and environmental data in order to characterize and understand complex human diseases on a network level, and to use that data to advance information-driven medicine and to better diagnose and treat patients at Mount Sinai Hospital, New York and elsewhere. (wikipedia.org)
  • bacteria
  • People have had some success in modeling specific regulatory networks in bacteria or yeast at a qualitative level, but no general approach has emerged. (macdevcenter.com)
  • Collado-Vides' research focuses on the regulation of gene expression in bacteria, in particular, creating a model of the regulatory network of E. coli K-12. (wikipedia.org)
  • This study provided comprehensive insights to the xylose catabolism and its regulation in diverse Firmicutes bacteria especially Clostridia species, and paved ways for improving xylose utilization capability in C. acetobutylicum by genetic engineering in the future. (springer.com)
  • Few such networks are known in anything approaching their complete structure, even in the simplest bacteria. (wikipedia.org)
  • Metabolism
  • These include intriguing instances of differing motif dosages and differing combinatorial motif control that promote regulatory specificity in rRNA metabolism under differing physiological processes. (nih.gov)
  • regulators
  • In order to identify molecules representing putative key regulators for diagnosis and therapeutic intervention, we analyzed gene expression and microRNA (miR) levels in OA and normal knee cartilage using a customized cartilage cDNA array and quantitative RT-PCR. (ebscohost.com)
  • data
  • Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis. (omicsoft.com)
  • In his last position, he worked as a bioinformatics scientist at National Institute of Health (NIH), studying statistical methods for Affymetrix and Next Generation Sequencing data. (omicsoft.com)
  • Now they are getting to the really fun part and have assembled all of their data into a network that resembles an electronic circuit with a series of gates. (macdevcenter.com)
  • To demonstrate its capabilities, we applied ORTI to gene expression data and identified modulated TFs using an enrichment analysis. (garvan.org.au)
  • The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. (biomedcentral.com)
  • In the following, we discuss some existing methods that have been proposed and implemented for the simulation of gene expression data. (biomedcentral.com)
  • 2015). Meta-analysis of RNA-seq expression data across species, tissues and studies. (mit.edu)
  • Quantitative visualization of alternative exon expression from RNA-seq data. (mit.edu)
  • Research in computational epigenetics comprises the development and application of bioinformatics methods for solving epigenetic questions, as well as computational data analysis and theoretical modeling in the context of epigenetics. (wikipedia.org)
  • The method's founders claim that it is a better way to find associations between MSigDB gene sets and microarray data. (wikipedia.org)
  • Her PhD work used machine learning and Bayesian networks to automatically infer regulatory relations between genes, using genomics data. (wikipedia.org)
  • Data objects in the EcoCyc database describe each E. coli gene and gene product. (wikipedia.org)
  • The six major data types in RGD are as follows: Genes: Initial gene records are imported/updated from the National Center for Biotechnology Information's (NCBI's) Gene database on a weekly basis. (wikipedia.org)
  • novel
  • SegCorr is a novel method that performs correlation matrix segmentation and applies a test procedure in order to detect highly correlated regions in gene expression. (biomedcentral.com)
  • Novel genes and their protein products that are expressed during the process are under active investigation in many laboratories. (wikipedia.org)
  • Modeling
  • The first relates to the connection structure among the genes and the second to the parameter values of the modeling equations. (biomedcentral.com)
  • regulons
  • XylR regulons were reconstructed by identification and comparative analysis of XylR-binding sites upstream of xylose and xyloside utilization genes. (springer.com)
  • metabolic
  • Stress-induced regulation of H19 expression by hypoxic signaling and inflammation suggests that lncRNA H19 acts as a metabolic correlate in cartilage and cultured chondrocytes, while the miR-675 may indirectly influence COL2A1 levels. (ebscohost.com)
  • Yeast
  • Thus a yeast cell, finding itself in a sugar solution, will turn on genes to make enzymes that process the sugar to alcohol. (wikipedia.org)
  • promoter
  • A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas Melloul et al. (wikipedia.org)
  • The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter. (wikipedia.org)
  • Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output). (wikipedia.org)
  • By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. (wikipedia.org)
  • Although it is not yet clearly understood, it is thought that the reverse transcript guides methylation complexes and/or histone-modifying complexes to the promoter regions of the sense transcript and cause an inhibition of expression from the gene. (wikipedia.org)
  • During the process of transcription of cis-NATs, the transcriptional complexes assemble in the promoter regions of the gene. (wikipedia.org)
  • subsequently
  • She was subsequently a postdoctoral research fellow in the lab of George M. Church in the Department of Genetics at Harvard Medical School, focusing on how genetic variation changes the regulatory network between individuals and how this subsequently manifests in phenotypic diversity. (wikipedia.org)
  • transcription factor bindi
  • Cis-regulatory modules are non-random clusters at their specified target site that contain transcription factor binding sites. (wikipedia.org)
  • However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators. (wikipedia.org)